With the Iron Dominion's assault focused on New Mobotropolis, Knuckles took it upon himself to hunt down Dr. Finitevus so as to learn his secrets and bring him to justice. This occurred after General Stryker sent him a summons, leading to a meeting at the Dingo camp. After revealing that his forces had uncovered Finitevus' lab and details on Project Enerjak: Reborn, Stryker dismissed any claims Knuckles had of guilt in the matter. With the General's help, Knuckles set out on his hunt with Julie-Su and Mighty for backup. After being dropped off in Sandopolis by their old friend Harry, the trio discovered a collection of ruins, some of which had been built by Echidnas. However, they then fell victim to a booby trap hidden inside one of the structures. Escaping, they traveled through an active Warp Ring to Downunda, where they found Dr. Finitevus at work. They attacked him, but Angel Island was then caught by chains rising from the Great Crater. Knuckles and the others were then offered a deal: attack Finitevus, or work with him in order to save Angel Island. (SU: #9, #10)

Knuckles' initial response was to attack Finitevus and demand answers regarding his plans and base which remained a mystery to him. Dr. Finitevus claimed innocence in the attack, refuted any right of Knuckles to question where he chose to locate himself and attributed lack of knowledge about the ruins to a lack in Knuckles' education as a Guardian. Knuckles, still confused and angry, retorted that he had a team in place to protect the Master Emerald from Finitevus, only for said team-Vector and Ray the Flying Squirrel-to emerge from a Warp Ring. The group was then attacked by a group of Wing Dingoes, and despite Knuckles' objections Finitevus stood with them. They received assistance from the Downunda Freedom Fighters. After dealing with the dingoes, the group rested within a ruined hut to get acquainted. Knuckles told of his recent adventures and impressed the Freedom Fighter group. They explained they were facing the Downunda Dark Egg Legion led by a former member, Duck "Bill" Platypus. Knuckles then wished to stop the Legion and he and Walt Wallabee came up with a plan, taking into account that Finitevus was working with them. Knuckles then told Vector and Mighty that Guru was coming with them to take out the chains and sent Julie-Su and Ray to take care of the Master Emerald at Shrine Isle. Knuckles led his team to the Great Crater rim and when he approached a launcher, Legionnaires and Winged Dingoes appeared and captured the group. Knuckles awoke to find everyone captured and in the hands of Finitevus and Bill. Dr. Finitevus then revealed that despite having no love for the Eggman Empire, under either Eggman or the Iron Queen, he had sided with them in exchange for access to the Master Emerald. After Finitevus departed to secure the island, Bill surprised the group by releasing them, explaining that he had played along with his people's desire to side with Eggman in hopes of thwarting their efforts. (SU: #9, #10, #11)

Knuckles then led the two teams in a breakout, letting the Freedom Fighters take care of their home while Mighty launched him back up to Shrine Island. There he found Dr. Finitevus, who offered Knuckles a chance to join him in "saving the world" and the chance to learn things about his people that the Brotherhood would not or could not have told him. Despite the temptation, Knuckles refused and attacked, leading to a battle between the two that nearly resulted in Knuckles' defeat. Fortunately, Julie-Su arrived just in time to rescue him from his nemesis, whom he then threw off the island. After bidding farewell to the Freedom Fighters, the Chaotix returned to the freed Angel Island, Knuckles and Julie-Su sharing a tender moment as they discussed the likelihood of Finitevus' escape. (SU: #12)